It's not really an abuse.  It is, however, buggy.  It should be being applied *only* when the header contains unstructured text.  Unfortunately I made the choice to treat any header that doesn't have a specific parser as unstructured, and that was a wrong choice which should be fixed.  It is an interesting question what should be used as the default parser, though.  Suggestions and code are welcome :)

There should be specific header parsers for headers that contain message ids.  That was on my todo list but did not get done before my circumstances changed and my free-time focus moved away from python development work :(

The message_id parser exists.  In-Reply-To just needs to be declared in the header registry as a MessageIDHeader (not sure how that got missed).  Writing a Header class for References should be trivial, it's just a list of message ids.  That will fix those headers, and I suggest we do that asap.

Fixing the default-to-unstructured will take a bit more thought and should probably be split out into a separate issue.  I can review and give advice (though you may have to ping me directly) but I won't have time to write any code.